Re: Buffer overflow error

OK running into a similar error, this time using the grdmath command.
Here's the full command I'm running, with all filenames expanded:

*grdmath
/data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/icesat_trend_OFP_case11l_1k_no8dy_regridded_grounded.llhdot.grd
/data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/icesat_trend_OFP_case11l_1k_no8dy_regridded_grounded_basin1.1.llhdot.grd
AND =
/data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/temp.grd*


When I run this, I get a buffer overflow error. When I run this command
with the -V option (I'm using GMT4), I don't get the buffer overflow. So
what's going on? Is there an issue with the filenames being too long? And
why does the -V option alter the way grdmath executes?


Denis



On Wed, May 21, 2014 at 2:28 PM, Denis Felikson <[email protected]> wrote:

> Hi Paul,
>
> I'm using 4.5.9. This is really strange - I tried re-running the same
> command but couldn't reproduce the error.
>
>
> Denis
>
>
> On Mon, May 19, 2014 at 6:04 PM, Paul Wessel <[email protected]> wrote:
>
>> Hi Denis-
>>
>> I tried a surface job with -Lud -Lld and could not reproduce it.  What
>> GMT version are we talking about? Could you please rerun your example with
>> -V (GMT4) or -Vd (GMT 5) and send us the output?  Please expand what
>> $inputFile and $outputFile are. E.g., are they excessively long path names?
>>
>>
>> -p
>>
>> On May 19, 2014, at 8:38 AM, Denis Felikson <[email protected]> wrote:
>>
>> Yes, the variables are defined. Further, the $inputFile actually exists
>> (checked by putting an ls $inputFile before the surface command).
>>
>> Here are some more clues. I'm trying again to run the command manually.
>> When I use the -Lld and -Lud options, I get the buffer overflow error. When
>> I omit these options, the surface command executes properly and writes a
>> grid file.
>>
>>
>> Denis
>>
>>
>>
>> On Mon, May 19, 2014 at 12:27 PM, Eduardo A. Suárez <
>> [email protected]> wrote:
>>
>>> Hi,
>>>
>>> put a line with:
>>>
>>> echo "$inputFile $outputFile"
>>>
>>> before the surface call, just to check if $inputFile and $outputFile are
>>> defined in your script.
>>>
>>> Eduardo.-
>>>
>>>
>>> Quoting Denis Felikson <[email protected]>:
>>>
>>>  I'm experiencing a buffer overflow error when executing the following
>>>> surface command:
>>>>
>>>> surface $inputFile -G$outputFile -I100k -R0/360/-90/-60 -T0.25 -Lld -Lud
>>>>
>>>> What's odd is that I see the error when I run this command in my shell
>>>> script. If I run it manually from the command line, everything works.
>>>>
>>>> Here's some system info. Let me know if there's any other information
>>>> needed:
>>>>
>>>> Linux version 2.6.32-131.4.1.el6.x86_64 (
>>>> [email protected]) (gcc version 4.4.5 20110214
>>>> (Red
>>>> Hat 4.4.5-6) (GCC) ) #1 SMP Fri Jun 10 10:54:26 EDT 2011
>>>>
>>>> And here's the error itself:
>>>>
>>>> *** buffer overflow detected ***: surface terminated
>>>> ======= Backtrace: =========
>>>> /lib64/libc.so.6(__fortify_fail+0x37)[0x3f45701307]
>>>> /lib64/libc.so.6[0x3f456ff1f0]
>>>> /lib64/libc.so.6[0x3f456fe0a7]
>>>> /usr/lib64/libgmt.so.4(GMT_grd_init+0xd6)[0x3608e2bd96]
>>>> surface[0x4066d5]
>>>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x3f4561ecdd]
>>>> surface[0x401439]
>>>> ======= Memory map: ========
>>>> 00400000-0040a000 r-xp 00000000 fd:05 9700262
>>>>  /usr/bin/surface
>>>> 00609000-00613000 rw-p 00009000 fd:05 9700262
>>>>  /usr/bin/surface
>>>> 01de0000-01e22000 rw-p 00000000 00:00 0
>>>>  [heap]
>>>> 3056400000-305641d000 r-xp 00000000 fd:01 2621513
>>>>  /lib64/libselinux.so.1
>>>> 305641d000-305661c000 ---p 0001d000 fd:01 2621513
>>>>  /lib64/libselinux.so.1
>>>> 305661c000-305661d000 r--p 0001c000 fd:01 2621513
>>>>  /lib64/libselinux.so.1
>>>> 305661d000-305661e000 rw-p 0001d000 fd:01 2621513
>>>>  /lib64/libselinux.so.1
>>>> 305661e000-305661f000 rw-p 00000000 00:00 0
>>>> 305c000000-305c02a000 r-xp 00000000 fd:01 2621915
>>>>  /lib64/libk5crypto.so.3.1
>>>> 305c02a000-305c22a000 ---p 0002a000 fd:01 2621915
>>>>  /lib64/libk5crypto.so.3.1
>>>> 305c22a000-305c22c000 rw-p 0002a000 fd:01 2621915
>>>>  /lib64/libk5crypto.so.3.1
>>>> 305c400000-305c4d4000 r-xp 00000000 fd:01 2621916
>>>>  /lib64/libkrb5.so.3.3
>>>> 305c4d4000-305c6d4000 ---p 000d4000 fd:01 2621916
>>>>  /lib64/libkrb5.so.3.3
>>>> 305c6d4000-305c6df000 rw-p 000d4000 fd:01 2621916
>>>>  /lib64/libkrb5.so.3.3
>>>> 305c800000-305c802000 r-xp 00000000 fd:01 2621486
>>>>  /lib64/libkeyutils.so.1.3
>>>> 305c802000-305ca01000 ---p 00002000 fd:01 2621486
>>>>  /lib64/libkeyutils.so.1.3
>>>> 305ca01000-305ca02000 rw-p 00001000 fd:01 2621486
>>>>  /lib64/libkeyutils.so.1.3
>>>> 305cc00000-305cc0a000 r-xp 00000000 fd:01 2621914
>>>>  /lib64/libkrb5support.so.0.1
>>>> 305cc0a000-305ce09000 ---p 0000a000 fd:01 2621914
>>>>  /lib64/libkrb5support.so.0.1
>>>> 305ce09000-305ce0a000 rw-p 00009000 fd:01 2621914
>>>>  /lib64/libkrb5support.so.0.1
>>>> 305d000000-305d03f000 r-xp 00000000 fd:01 2621920
>>>>  /lib64/libgssapi_krb5.so.2.2
>>>> 305d03f000-305d23e000 ---p 0003f000 fd:01 2621920
>>>>  /lib64/libgssapi_krb5.so.2.2
>>>> 305d23e000-305d241000 rw-p 0003e000 fd:01 2621920
>>>>  /lib64/libgssapi_krb5.so.2.2
>>>> 305d400000-305d407000 r-xp 00000000 fd:01 2621918
>>>>  /lib64/libcrypt-2.12.so
>>>> 305d407000-305d607000 ---p 00007000 fd:01 2621918
>>>>  /lib64/libcrypt-2.12.so
>>>> 305d607000-305d608000 r--p 00007000 fd:01 2621918
>>>>  /lib64/libcrypt-2.12.so
>>>> 305d608000-305d609000 rw-p 00008000 fd:01 2621918
>>>>  /lib64/libcrypt-2.12.so
>>>> 305d609000-305d637000 rw-p 00000000 00:00 0
>>>> 305d800000-305d85d000 r-xp 00000000 fd:01 2621870
>>>>  /lib64/libfreebl3.so
>>>> 305d85d000-305da5c000 ---p 0005d000 fd:01 2621870
>>>>  /lib64/libfreebl3.so
>>>> 305da5c000-305da5e000 rw-p 0005c000 fd:01 2621870
>>>>  /lib64/libfreebl3.so
>>>> 305da5e000-305da62000 rw-p 00000000 00:00 0
>>>> 305dc00000-305dc38000 r-xp 00000000 fd:01 2621921
>>>>  /lib64/libnspr4.so
>>>> 305dc38000-305de38000 ---p 00038000 fd:01 2621921
>>>>  /lib64/libnspr4.so
>>>> 305de38000-305de3a000 rw-p 00038000 fd:01 2621921
>>>>  /lib64/libnspr4.so
>>>> 305de3a000-305de3d000 rw-p 00000000 00:00 0
>>>> 305e400000-305e533000 r-xp 00000000 fd:05 9446798
>>>>  /usr/lib64/libnss3.so
>>>> 305e533000-305e733000 ---p 00133000 fd:05 9446798
>>>>  /usr/lib64/libnss3.so
>>>> 305e733000-305e73a000 rw-p 00133000 fd:05 9446798
>>>>  /usr/lib64/libnss3.so
>>>> 305e73a000-305e73b000 rw-p 00000000 00:00 0
>>>> 305e800000-305e81a000 r-xp 00000000 fd:05 9437512
>>>>  /usr/lib64/libnssutil3.so
>>>> 305e81a000-305ea19000 ---p 0001a000 fd:05 9437512
>>>>  /usr/lib64/libnssutil3.so
>>>> 305ea19000-305ea1f000 rw-p 00019000 fd:05 9437512
>>>>  /usr/lib64/libnssutil3.so
>>>> 305ec00000-305ec04000 r-xp 00000000 fd:01 2621922
>>>>  /lib64/libplc4.so
>>>> 305ec04000-305ee03000 ---p 00004000 fd:01 2621922
>>>>  /lib64/libplc4.so
>>>> 305ee03000-305ee04000 rw-p 00003000 fd:01 2621922
>>>>  /lib64/libplc4.so
>>>> 305f000000-305f003000 r-xp 00000000 fd:01 2621923
>>>>  /lib64/libplds4.so
>>>> 305f003000-305f202000 ---p 00003000 fd:01 2621923
>>>>  /lib64/libplds4.so
>>>> 305f202000-305f203000 rw-p 00002000 fd:01 2621923
>>>>  /lib64/libplds4.so
>>>> 305f400000-305f428000 r-xp 00000000 fd:05 9446800
>>>>  /usr/lib64/libsmime3.so
>>>> 305f428000-305f628000 ---p 00028000 fd:05 9446800
>>>>  /usr/lib64/libsmime3.so
>>>> 305f628000-305f62c000 rw-p 00028000 fd:05 9446800
>>>>  /usr/lib64/libsmime3.so
>>>> 3060400000-3060419000 r-xp 00000000 fd:05 9446801
>>>>  /usr/lib64/libsasl2.so.2.0.23
>>>> 3060419000-3060619000 ---p 00019000 fd:05 9446801
>>>>  /usr/lib64/libsasl2.so.2.0.23
>>>> 3060619000-306061a000 rw-p 00019000 fd:05 9446801
>>>>  /usr/lib64/libsasl2.so.2.0.23
>>>> 3061c00000-3061c8c000 r-xp 00000000 fd:05 9437461
>>>>  /usr/lib64/libsqlite3.so.0.8.6
>>>> 3061c8c000-3061e8b000 ---p 0008c000 fd:05 9437461
>>>>  /usr/lib64/libsqlite3.so.0.8.6
>>>> 3061e8b000-3061e8f000 rw-p 0008b000 fd:05 9437461
>>>>  /usr/lib64/libsqlite3.so.0.8.6
>>>> 32dde00000-32dde41000 r-xp 00000000 fd:05 9446895
>>>>  /usr/lib64/libproj.so.0.6.6
>>>> 32dde41000-32de040000 ---p 00041000 fd:05 9446895
>>>>  /usr/lib64/libproj.so.0.6.6
>>>> 32de040000-32de043000 rw-p 00040000 fd:05 9446895
>>>>  /usr/lib64/libproj.so.0.6.6
>>>> 32de600000-32de610000 r-xp 00000000 fd:05 9446846
>>>>  /usr/lib64/libodbcinst.so.2.0.0
>>>> 32de610000-32de810000 ---p 00010000 fd:05 9446846
>>>>  /usr/lib64/libodbcinst.so.2.0.0
>>>>
>>>> Mailing list for GMT discussions of all kinds.  If you are not sure
>>>>  you have found a bug, discuss it here first.
>>>> To formally report bugs or request features, please register and add
>>>>  New Issue on gmt.soest.hawaii.edu
>>>> To unsubscribe, send the message "signoff gmt-help" to
>>>> [email protected]
>>>> Note: gmt-help will become obsolete on Sept 1, 2014 - please use  forum
>>>> on gmt.soest.hawaii.edu instead.
>>>>
>>>>
>>>
>>>
>>> --
>>> Eduardo A. Suarez
>>> Facultad de Ciencias Astronómicas y Geofísicas - UNLP
>>> FCAG: (0221)-4236593 int. 172/Cel: (0221)-15-4557542/Casa: (0221)-4526589
>>>
>>>
>>> ----------------------------------------------------------------
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>>>
>>> Mailing list for GMT discussions of all kinds.  If you are not sure you
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>>>
>>
>> Mailing list for GMT discussions of all kinds. If you are not sure you
>> have found a bug, discuss it here first. To formally report bugs or request
>> features, please register and add New Issue on gmt.soest.hawaii.edu To
>> unsubscribe, send the message "signoff gmt-help" to
>> [email protected] Note: gmt-help will become obsolete on Sept 1,
>> 2014 - please use forum on gmt.soest.hawaii.edu instead.
>>
>>
>> Mailing list for GMT discussions of all kinds. If you are not sure you
>> have found a bug, discuss it here first. To formally report bugs or request
>> features, please register and add New Issue on gmt.soest.hawaii.edu To
>> unsubscribe, send the message "signoff gmt-help" to
>> [email protected] Note: gmt-help will become obsolete on Sept 1,
>> 2014 - please use forum on gmt.soest.hawaii.edu instead.
>>
>
>

Mailing list for GMT discussions of all kinds.  If you are not sure you have found a bug, discuss it here first.
To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu
To unsubscribe, send the message "signoff gmt-help" to [email protected]
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.